Graph based gene/protein prediction and clustering over uncertain medical databases.

Clustering over protein or gene data is now a popular issue in biomedical databases. In general, large sets of gene tags are clustered using high computation techniques over gene or protein distributed data. Most of the traditional clustering techniques are based on subspace, hierarchical and partitioning feature extraction. Various clustering techniques have been proposed in the literature with different cluster measures, but their performance is limited due to spatial noise and uncertainty. In this paper, an improved graph-based clustering technique is proposed for the generation of efficient gene or protein clusters over uncertain and noisy data. The proposed graph-based visualization can effectively identify different types of genes or proteins along with relational attributes. Experimental results show that the proposed graph model more effectively clusters complex gene or protein data when compared with conventional clustering approaches

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

DeepSF: deep convolutional neural network for mapping protein sequences to folds

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice. Results We develop a deep 1D-convolution neural network (DeepSF) to directly classify any protein se quence into one of 1195 known folds, which is useful for both fold recognition and the study of se quence-structure relationship. Different from traditional sequence alignment (comparison) based methods, our method automatically extracts fold-related features from a protein sequence of any length and map it to the fold space. We train and test our method on the datasets curated from SCOP1.75, yielding a classification accuracy of 80.4%. On the independent testing dataset curated from SCOP2.06, the classification accuracy is 77.0%. We compare our method with a top profile profile alignment method - HHSearch on hard template-based and template-free modeling targets of CASP9-12 in terms of fold recognition accuracy. The accuracy of our method is 14.5%-29.1% higher than HHSearch on template-free modeling targets and 4.5%-16.7% higher on hard template-based modeling targets for top 1, 5, and 10 predicted folds. The hidden features extracted from sequence by our method is robust against sequence mutation, insertion, deletion and truncation, and can be used for other protein pattern recognition problems such as protein clustering, comparison and ranking.Comment: 28 pages, 13 figure

An Overview of the Use of Neural Networks for Data Mining Tasks

In the recent years the area of data mining has experienced a considerable demand for technologies that extract knowledge from large and complex data sources. There is a substantial commercial interest as well as research investigations in the area that aim to develop new and improved approaches for extracting information, relationships, and patterns from datasets. Artificial Neural Networks (NN) are popular biologically inspired intelligent methodologies, whose classification, prediction and pattern recognition capabilities have been utilised successfully in many areas, including science, engineering, medicine, business, banking, telecommunication, and many other fields. This paper highlights from a data mining perspective the implementation of NN, using supervised and unsupervised learning, for pattern recognition, classification, prediction and cluster analysis, and focuses the discussion on their usage in bioinformatics and financial data analysis tasks

Feature Extraction from Degree Distribution for Comparison and Analysis of Complex Networks

The degree distribution is an important characteristic of complex networks. In many data analysis applications, the networks should be represented as fixed-length feature vectors and therefore the feature extraction from the degree distribution is a necessary step. Moreover, many applications need a similarity function for comparison of complex networks based on their degree distributions. Such a similarity measure has many applications including classification and clustering of network instances, evaluation of network sampling methods, anomaly detection, and study of epidemic dynamics. The existing methods are unable to effectively capture the similarity of degree distributions, particularly when the corresponding networks have different sizes. Based on our observations about the structure of the degree distributions in networks over time, we propose a feature extraction and a similarity function for the degree distributions in complex networks. We propose to calculate the feature values based on the mean and standard deviation of the node degrees in order to decrease the effect of the network size on the extracted features. The proposed method is evaluated using different artificial and real network datasets, and it outperforms the state of the art methods with respect to the accuracy of the distance function and the effectiveness of the extracted features.Comment: arXiv admin note: substantial text overlap with arXiv:1307.362